# A treemap R script produced by the REVIGO server at http://revigo.irb.hr/
# If you found REVIGO useful in your work, please cite the following reference:
# Supek F et al. "REVIGO summarizes and visualizes long lists of Gene Ontology
# terms" PLoS ONE 2011. doi:10.1371/journal.pone.0021800
# author: Anton Kratz <anton.kratz@gmail.com>, RIKEN Omics Science Center, Functional Genomics Technology Team, Japan
# created: Fri, Nov 02, 2012 7:25:52 PM
# last change: Fri, Nov 09, 2012 3:20:01 PM
# If you don't have the treemap package installed, uncomment the following line:
# install.packages( "treemap" );
library(treemap) # treemap package by Martijn Tennekes
library(tidyverse)
library(ggrepel)
library(ggnewscale)
library(cowplot)
library(eulerr)
# Data from REVIGO. Scroll down for plot configuration options.
# Prep data from Revigo for analysis by removing 4 lines above header
# tail -n +5 DEDS_ab_BP_parchild_REVIGO_treemap.csv > file.txt.new && mv file.txt.new DEDS_ab_BP_parchild_REVIGO_treemap.csv
#set working directory
setwd("~/OneDrive/B_anynana_altSplicing/PanicTime/genelists/REVIGO_F/treemap/")
#setwd("~/OneDrive/B_anynana_altSplicing/B_anynana_GSEA/edgeRDEvsDS/Treemap/")
revigo.names <- c("TermID","Name","Frequency","Value","Uniqueness","Dispensability","Representative");
temp_revigo <- list.files(pattern="*.csv")
my_names <- str_sub(temp_revigo, end = -5)
my_revigo <- lapply(temp_revigo, read.csv)
names(my_revigo) <- my_names
names(my_revigo[1])
## [1] "ab_DE_F_BP.REVIGO.treemap"
for (i in 1:length(my_revigo)) {
revigo.data <- my_revigo[[i]]
revigo.data$absValue <- abs(revigo.data$Value)
# by default, outputs to a PDF file
pdf(file= paste(names(my_revigo[i]),"revigo_treemap_simple.pdf", sep = "_"), width=8, height=4.5 )# width=16, height=9 ) # width and height are in inches
# check the tmPlot command documentation for all possible parameters - there are a lot more
treemap(
revigo.data,
index = c("Representative"), #,"Name"),
vSize = "absValue",
type = "categorical",
vColor = "Representative",
title = names(my_revigo[i]),
inflate.labels = FALSE, # set this to TRUE for space-filling group labels - good for posters
lowerbound.cex.labels = 0, # try to draw as many labels as possible (still, some small squares may not get a label)
bg.labels = "#CCCCCCAA", # define background color of group labels
# "#CCCCCC00" is fully transparent, "#CCCCCCAA" is semi-transparent grey, NA is opaque
position.legend = "none"
)
dev.off()
pdf(file= paste(names(my_revigo[i]),"revigo_treemap.pdf", sep = "_"), width=8, height=4.5 )# width=16, height=9 ) # width and height are in inches
# check the tmPlot command documentation for all possible parameters - there are a lot more
treemap(
revigo.data,
index = c("Representative","Name"),
vSize = "absValue",
type = "categorical",
vColor = "Representative",
title = names(my_revigo[i]),
inflate.labels = FALSE, # set this to TRUE for space-filling group labels - good for posters
lowerbound.cex.labels = 0, # try to draw as many labels as possible (still, some small squares may not get a label)
bg.labels = "#CCCCCCAA", # define background color of group labels
# "#CCCCCC00" is fully transparent, "#CCCCCCAA" is semi-transparent grey, NA is opaque
position.legend = "none"
)
dev.off()
}
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
## Warning in if (class(try(col2rgb(bg.labels), silent = TRUE)) == "try-error") stop("Invalid bg.labels"): the condition has length > 1 and only the first element will be
## used
## Warning in `[.data.table`(dtfDT, , `:=`("c", fact), with = FALSE): with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples.
warnings()
## Warning messages:
## 1: In in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, ... :
## You changed the working directory to /Users/rachelsteward/OneDrive/B_anynana_altSplicing/PanicTime/genelists/REVIGO_F/SemSpace/all (probably via setwd()). It will be restored to /Users/rachelsteward/OneDrive/B_anynana_altSplicing/PanicTime. See the Note section in ?knitr::knit
## 2: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## 3: ggrepel: 12 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## 4: ggrepel: 7 unlabeled data points (too many overlaps). Consider increasing max.overlaps
#### Semantic space ####
# setwd("~/OneDrive/B_anynana_altSplicing/B_anynana_GSEA/DEvsAllDS/parentChild/REVIGO/SemSpace/")
setwd("/Users/rachelsteward/OneDrive/B_anynana_altSplicing/PanicTime/genelists/REVIGO_F/SemSpace/")
semspace.names <- c("TermID","Name","Frequency","PlotX","PlotY","PlotSize","Value","Uniqueness","Dispensability","Representative", "Eliminated")
temp_semspace <- list.files(pattern="*.csv")
my_names <- str_sub(temp_semspace, end = -5)
my_semspace <- lapply(temp_semspace, read.csv)
names(my_semspace) <- my_names
names(my_semspace[1])
## [1] "ab_DE_F_BP.REVIGO"
plots <- vector('list', length(my_semspace))
for (i in 1:length(my_semspace)) {
my_semspace[[i]] <- my_semspace[[i]] [(my_semspace[[i]]$PlotX != "null" & my_semspace[[i]]$PlotY != "null"), ];
my_semspace[[i]]$PlotX <- as.numeric( as.character(my_semspace[[i]]$PlotX) );
my_semspace[[i]]$PlotY <- as.numeric( as.character(my_semspace[[i]]$PlotY) );
my_semspace[[i]]$PlotSize <- as.numeric( as.character(my_semspace[[i]]$PlotSize) );
my_semspace[[i]]$Value <- as.numeric( as.character(my_semspace[[i]]$Value) );
my_semspace[[i]]$Frequency <- as.numeric(as.numeric(sub("%", "",my_semspace[[i]]$Frequency,fixed=TRUE))/100);
my_semspace[[i]]$Uniqueness <- as.numeric( as.character(my_semspace[[i]]$Uniqueness) );
my_semspace[[i]]$Dispensability <- as.numeric( as.character(my_semspace[[i]]$Dispensability) );
my_semspace[[i]]$name <- names(my_semspace[i])
ex <- my_semspace[[i]] [ my_semspace[[i]]$Dispensability < 0.15 & my_semspace[[i]]$Value < log10(0.05), ]
one.x_range = max(my_semspace[[i]]$PlotX) - min(my_semspace[[i]]$PlotX);
one.y_range = max(my_semspace[[i]]$PlotY) - min(my_semspace[[i]]$PlotY);
p1 <- ggplot( data = my_semspace[[i]][ my_semspace[[i]]$Value < log10(0.05), ] ) +
geom_point( aes( PlotX, PlotY, colour = Value, size = PlotSize), alpha = I(0.6) ) +
scale_colour_gradientn( colours = c("blue", "green", "yellow", "red") , limits = c( -6, 0))+
geom_point( aes(PlotX, PlotY, size = PlotSize), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) +
scale_size( range=c(5, 30), guide = FALSE) +
theme_bw() +
geom_text( data = ex, aes(PlotX, PlotY, label = Name), colour = I(alpha("black", 0.85)), size = 3 ) +
labs (y = "Semantic space x", x = "Semantic space y") + theme(legend.key = element_blank()) +
xlim(min(my_semspace[[i]]$PlotX)-one.x_range/10,max(my_semspace[[i]]$PlotX)+one.x_range/10) +
ylim(min(my_semspace[[i]]$PlotY)-one.y_range/10,max(my_semspace[[i]]$PlotY)+one.y_range/10);
ggsave(plot = p1, file= paste0(names(my_semspace[i]),".pdf"), width=9, height=9 ) # width and height are in inches
# "#7876B1","#0072B5","#BC3C29"
semspace.colors <- c("#0072B5","#0072B5",
"#7876B1","#7876B1",
"#BC3C29","#BC3C29",
"#0072B5","#0072B5",
"#7876B1","#7876B1",
"#BC3C29","#BC3C29")
message(i)
plots[[i]] <- local({
p1 <- ggplot( ) +
geom_point(data = my_semspace[[i]][ my_semspace[[i]]$Value < log10(0.05), ], aes( PlotX, PlotY, size = PlotSize, alpha = -(Value)), colour = semspace.colors[i] ) +
geom_point( data = my_semspace[[i]][ my_semspace[[i]]$Value < log10(0.05), ], aes(PlotX, PlotY, size = PlotSize), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) +
scale_colour_gradient(limits = c( -6, 0))+
scale_size( range=c(5, 20), guide = FALSE) +
theme_bw() +
geom_text_repel( data = my_semspace[[i]][ my_semspace[[i]]$Dispensability < 0.1 & my_semspace[[i]]$Value < log10(0.05), ],
aes(PlotX, PlotY, label = Name), colour = I(alpha("black", 0.85)), size = 4, ) +
labs (y = "Semantic space x", x = "Semantic space y") + theme(legend.key = element_blank()) +
xlim(-9, 9) +
ylim(-9,9) +
theme(legend.position = "bottom")
print(p1)
})
}
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 114 rows containing missing values (geom_point).
## Warning: Removed 114 rows containing missing values (geom_point).
## 1
## Warning: Removed 114 rows containing missing values (geom_point).
## Warning: Removed 114 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 14 rows containing missing values (geom_point).
## Warning: Removed 14 rows containing missing values (geom_point).
## 2
## Warning: Removed 14 rows containing missing values (geom_point).
## Warning: Removed 14 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 107 rows containing missing values (geom_point).
## Warning: Removed 107 rows containing missing values (geom_point).
## 3
## Warning: Removed 107 rows containing missing values (geom_point).
## Warning: Removed 107 rows containing missing values (geom_point).
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Removed 8 rows containing missing values (geom_point).
## 4
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## 5
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## 6
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 37 rows containing missing values (geom_point).
## Warning: Removed 37 rows containing missing values (geom_point).
## 7
## Warning: Removed 37 rows containing missing values (geom_point).
## Warning: Removed 37 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Removed 10 rows containing missing values (geom_point).
## 8
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## 9
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## 10
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: Removed 43 rows containing missing values (geom_point).
## Warning: Removed 43 rows containing missing values (geom_point).
## 11
## Warning: Removed 43 rows containing missing values (geom_point).
## Warning: Removed 43 rows containing missing values (geom_point).
## 12
names(my_semspace)
## [1] "ab_DE_F_BP.REVIGO" "ab_DE_F_MF.REVIGO" "ab_DEDS_F_BP.REVIGO" "ab_DEDS_F_MF.REVIGO" "ab_DS_F_BP.REVIGO" "ab_DS_F_MF.REVIGO" "th_DE_F_BP.REVIGO"
## [8] "th_DE_F_MF.REVIGO" "th_DEDS_F_BP.REVIGO" "th_DEDS_F_MF.REVIGO" "th_DS_F_BP.REVIGO" "th_DS_F_MF.REVIGO"
ab_BP <- plot_grid(plots[[1]]+ theme(legend.position = "none"),
plots[[3]]+ theme(legend.position = "none"),
plots[[5]]+ theme(legend.position = "none"),
NULL,
cowplot::get_legend(plots[[9]]),
NULL,
ncol = 3, nrow =2, labels = c("A", "B", "C", ""),
rel_widths = c(1,1,1), rel_heights = c(1,.1))
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 114 rows containing missing values (geom_point).
## Warning: Removed 114 rows containing missing values (geom_point).
## Warning: Removed 107 rows containing missing values (geom_point).
## Warning: Removed 107 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
ggsave(ab_BP, filename = "ab_BP_parchild_REVIGO_semspace.pdf", height = 7, width = 20)
th_BP <- plot_grid(plots[[7]]+ theme(legend.position = "none"), #DE
plots[[9]]+ theme(legend.position = "none"), #DEDS
plots[[11]]+ theme(legend.position = "none"), #DS
NULL,
cowplot::get_legend(plots[[11]]),
NULL,
ncol = 3, nrow =2, labels = c("D", "E", "F", ""),
rel_widths = c(1,1,1), rel_heights = c(1,.1))
## Warning: Removed 43 rows containing missing values (geom_point).
## Warning: Removed 43 rows containing missing values (geom_point).
## Warning: Removed 37 rows containing missing values (geom_point).
## Warning: Removed 37 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 27 rows containing missing values (geom_point).
## Warning: Removed 43 rows containing missing values (geom_point).
## Warning: Removed 43 rows containing missing values (geom_point).
ggsave(th_BP, filename = "th_BP_parchild_REVIGO_semspace.pdf", height = 7, width = 20)
ab_MF <- plot_grid(plots[[2]]+ theme(legend.position = "none"),
plots[[4]]+ theme(legend.position = "none"),
plots[[6]]+ theme(legend.position = "none"),
NULL,
cowplot::get_legend(plots[[10]]),
NULL,
ncol = 3, nrow =2, labels = c("A", "B", "C", ""),
rel_widths = c(1,1,1), rel_heights = c(1,.1))
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 14 rows containing missing values (geom_point).
## Warning: Removed 14 rows containing missing values (geom_point).
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Removed 8 rows containing missing values (geom_point).
ggsave(ab_MF, filename = "ab_MF_parchild_REVIGO_semspace.pdf", height = 7, width = 20)
th_MF <- plot_grid(plots[[8]]+ theme(legend.position = "none"),
plots[[10]]+ theme(legend.position = "none"),
plots[[12]]+ theme(legend.position = "none"),
NULL,
cowplot::get_legend(plots[[12]]),
NULL,
ncol = 3, nrow =2, labels = c("D", "E", "F", ""),
rel_widths = c(1,1,1), rel_heights = c(1,.1))
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
ggsave(th_MF, filename = "th_MF_parchild_REVIGO_semspace.pdf", height = 7, width = 20)
my_names <- names(my_semspace)
for (i in 1:length(my_semspace)) {
my_revigo[[i]] <- my_semspace[[i]] %>% select(TermID, Value)
colnames(my_revigo[[i]]) <- c("TermID", my_names[i])
}
all_terms <- data.frame(my_revigo[[1]])
for (i in 2:length(temp_revigo)){
all_terms<- full_join(all_terms, my_revigo[[i]])
}
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
all_terms <- all_terms %>%
mutate_at(vars(-TermID), ~ if_else(.x<0.05,1,0)) %>%
mutate_at(vars(-TermID), ~ if_else(is.na(.x),0,.x))
semspace.colors2 <- c("#7876B1","#0072B5","#BC3C29")
#
# pdf(file ="eulerr_overlapping_GO_terms.pdf", height = 4, width = 4)
# plot(euler(all_terms[, c(3,1,5)], shape= "ellipse"),
# quantities = list(fontsize =16),
# fill = semspace.colors2, alpha = 0.85,
# labels = c( "DE-DS", "DE only","DS only") ,
# lty = 1, title = "AB_BP")
# # plot(venn(all_terms[, c(2,6,10)], labels = c( "DE-DS", "DE only","DS only"),fill = semspace.colors2, alpha = 0.85))
#
#
# plot(euler(all_terms[, c(4,2,6)], shape= "ellipse"),
# quantities = list(fontsize =16),
# fill = semspace.colors2, alpha = 0.85,
# labels = c( "DE-DS", "DE only","DS only") ,
# lty = 1, title = "AB_MF")
# # plot(venn(all_terms[, c(3,7,11)]),labels = c( "DE-DS", "DE only","DS only") , fill = semspace.colors2, alpha = 0.85)
#
# plot(euler(all_terms[, c(9,7,11)], shape= "ellipse"),
# quantities = list(fontsize =16),
# fill = semspace.colors2, alpha = 0.85,
# labels = c( "DE-DS", "DE only","DS only") ,
# lty = 1, title = "TH_BP")
#
# # plot(venn(all_terms[, c(4,8,12)]),labels = c( "DE-DS", "DE only","DS only") , fill = semspace.colors2, alpha = 0.85)
#
# plot(euler(all_terms[, c(10,8,12)], shape= "ellipse"),
# quantities = list(fontsize =16),
# fill = semspace.colors2, alpha = 0.85,
# labels = c( "DE-DS", "DE only","DS only") ,
# lty = 1)
# # plot(venn(all_terms[, c(5,9,13)]),labels = c( "DE-DS", "DE only","DS only") , fill = semspace.colors2, alpha = 0.85)
# dev.off()
ab_BP_overlap <- all_terms[, c(1,2,4,6)]%>% filter_at(vars(-TermID), any_vars(. > 0)) %>% mutate(sum = rowSums(.[2:4]), group = "ab_BP") %>% filter(sum >1)
colnames(ab_BP_overlap) <- c("termID", "DE", "DEDS", "DS", "sum", "group")
ab_MF_overlap <- all_terms[, c(1,3,5,7)] %>% filter_at(vars(-TermID), any_vars(. > 0))%>% mutate(sum = rowSums(.[2:4]), group = "ab_MF") %>% filter(sum >1)
colnames(ab_MF_overlap) <- c("termID", "DE", "DEDS", "DS", "sum", "group")
th_BP_overlap <- all_terms[, c(1,8,10,12)]%>% filter_at(vars(-TermID), any_vars(. > 0))%>% mutate(sum = rowSums(.[2:4]), group = "th_BP") %>% filter(sum >1)
colnames(th_BP_overlap) <- c("termID", "DE", "DEDS", "DS", "sum", "group")
th_MF_overlap <- all_terms[, c(1,9,11,13)]%>% filter_at(vars(-TermID), any_vars(. > 0))%>% mutate(sum = rowSums(.[2:4]), group = "th_MF") %>% filter(sum >1)
colnames(th_MF_overlap) <- c("termID", "DE", "DEDS", "DS", "sum", "group")
overlap <- union(ab_BP_overlap, ab_MF_overlap) %>% union(th_BP_overlap)%>% union(th_MF_overlap)
write.csv(overlap, "/Users/rachelsteward/OneDrive/B_anynana_altSplicing/PanicTime/genelists/REVIGO_F/overlappping_go_terms.csv")
setwd("/Users/rachelsteward/OneDrive/B_anynana_altSplicing/PanicTime/genelists/REVIGO_F/SemSpace/all/")
temp_combined <- list.files(pattern="*csv")
my_names <- str_sub(temp_combined, end = -12)
my_combined <- lapply(temp_combined, read.csv)
names(my_combined) <- my_names
names(my_combined)
## [1] "ab_F_BP" "ab_F_MF" "th_F_BP" "th_F_MF"
for (i in 1:length(my_combined)) {
my_combined[[i]] <- my_combined[[i]][,c(1,4,5)]
my_combined[[i]] <- my_combined[[i]] [(my_combined[[i]]$PlotX != "null" & my_combined[[i]]$PlotY != "null"), ];
my_combined[[i]]$PlotX <- as.numeric( as.character(my_combined[[i]]$PlotX) );
my_combined[[i]]$PlotY <- as.numeric( as.character(my_combined[[i]]$PlotY) )
}
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
my_semspace_ab_BP <- my_semspace[grepl("ab_DE_F_BP|ab_DEDS_F_BP|ab_DS_F_BP", names(my_semspace))]
my_semspace_th_BP <- my_semspace[grepl("th_DE_F_BP|th_DEDS_F_BP|th_DS_F_BP", names(my_semspace))]
my_semspace_ab_MF <- my_semspace[grepl("ab_DE_F_MF|ab_DEDS_F_MF|ab_DS_F_MF", names(my_semspace))]
my_semspace_th_MF <- my_semspace[grepl("th_DE_F_MF|th_DEDS_F_MF|th_DS_F_MF", names(my_semspace))]
combined_list <- list()
factorNum <- c("DE_only", "DE_DS", "DS_only")
for (i in 1:length(my_semspace_ab_BP)) {
my_semspace_ab_BP[[i]] <- my_semspace_ab_BP[[i]] %>%
dplyr::select(-c(PlotX, PlotY)) %>%
filter(Dispensability < 0.3) %>%
left_join(my_combined$ab_F_BP) %>% mutate(Name = as.character(Name))
my_semspace_ab_BP[[i]]$name <- factorNum[[i]]
combined_list$my_combined_ab_BP <-rbind(combined_list$my_combined_ab_BP, my_semspace_ab_BP[[i]])
}
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
combined_list$my_combined_ab_BP$textBreaks <- sapply(strsplit(combined_list$my_combined_ab_BP$Name, " "), function(x) {
spacePosition <- cumsum(nchar(x))
placeBreak <- spacePosition[which(diff(spacePosition %/% 50) == 1)] + 1
result <- paste(x, collapse = " ")
for(i in placeBreak) {
substring(result, i, i) <- "\n"
}
result
})
for (i in 1:length(my_semspace_th_BP)) {
my_semspace_th_BP[[i]] <- my_semspace_th_BP[[i]] %>% dplyr::select(-c(PlotX, PlotY)) %>% filter(Dispensability < 0.3) %>% left_join(my_combined$th_F_BP)%>% mutate(Name = as.character(Name))
my_semspace_th_BP[[i]]$name <- factorNum[[i]]
combined_list$my_combined_th_BP <-rbind(combined_list$my_combined_th_BP, my_semspace_th_BP[[i]])
}
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
combined_list$my_combined_th_BP$textBreaks <- sapply(strsplit(combined_list$my_combined_th_BP$Name, " "), function(x) {
spacePosition <- cumsum(nchar(x))
placeBreak <- spacePosition[which(diff(spacePosition %/% 50) == 1)] + 1
result <- paste(x, collapse = " ")
for(i in placeBreak) {
substring(result, i, i) <- "\n"
}
result
})
for (i in 1:length(my_semspace_ab_MF)) {
my_semspace_ab_MF[[i]] <- my_semspace_ab_MF[[i]] %>% dplyr::select(-c(PlotX, PlotY)) %>%filter(Dispensability < 0.3) %>% left_join(my_combined$ab_F_MF) %>% mutate(Name = as.character(Name))
my_semspace_ab_MF[[i]]$name <- factorNum[[i]]
combined_list$my_combined_ab_MF <-rbind(combined_list$my_combined_ab_MF, my_semspace_ab_MF[[i]])
}
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
combined_list$my_combined_ab_MF$textBreaks <- sapply(strsplit(combined_list$my_combined_ab_MF$Name, " "), function(x) {
spacePosition <- cumsum(nchar(x))
placeBreak <- spacePosition[which(diff(spacePosition %/% 50) == 1)] + 1
result <- paste(x, collapse = " ")
for(i in placeBreak) {
substring(result, i, i) <- "\n"
}
result
})
for (i in 1:length(my_semspace_th_MF)) {
my_semspace_th_MF[[i]] <- my_semspace_th_MF[[i]] %>% dplyr::select(-c(PlotX, PlotY)) %>%filter(Dispensability < 0.3) %>% left_join(my_combined$th_F_MF)%>% mutate(Name = as.character(Name))
my_semspace_th_MF[[i]]$name <- factorNum[[i]]
combined_list$my_combined_th_MF <-rbind(combined_list$my_combined_th_MF, my_semspace_th_MF[[i]])
}
## Joining, by = "TermID"
## Joining, by = "TermID"
## Joining, by = "TermID"
combined_list$my_combined_th_MF$textBreaks <- sapply(strsplit(combined_list$my_combined_th_MF$Name, " "), function(x) {
spacePosition <- cumsum(nchar(x))
placeBreak <- spacePosition[which(diff(spacePosition %/% 50) == 1)] + 1
result <- paste(x, collapse = " ")
for(i in placeBreak) {
substring(result, i, i) <- "\n"
}
result
})
semspace.colors2 <- c("#0072B5","#7876B1","#BC3C29")
semspace.colors3 <- c("dodgerblue4","orchid4","darkred")
plots2 <- vector('list', length(combined_list))
plots3 <- vector('list', length(combined_list))
names(combined_list)
## [1] "my_combined_ab_BP" "my_combined_th_BP" "my_combined_ab_MF" "my_combined_th_MF"
for (i in 1:length(combined_list)){
message(i)
plots2[[i]] <- local({
p1 <- ggplot( ) +
geom_point(data = combined_list[[i]], aes( PlotX, PlotY, size = PlotSize, colour = name ), alpha =0.75) +
geom_point( data = combined_list[[i]], aes(PlotX, PlotY, size = PlotSize), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) +
scale_color_manual(values = semspace.colors2[c(2,1,3)],
labels = c("DE & DS","DE only", "DS only"))+
scale_size( range=c(5, 20), guide = FALSE) +
theme_minimal(base_size = 15) +
new_scale_color() +
#geom_text_repel( data = combined_list[[i]][combined_list[[i]]$Dispensability < 0.001, ],
#aes(PlotX, PlotY, label = Name, colour = name), size = 4 ) +
geom_text_repel(
data = na.omit(combined_list[[i]][combined_list[[i]]$PlotX > 0 & combined_list[[i]]$Dispensability < 0.1,]),
aes(PlotX, PlotY, label = Name, colour = name), size = 3.5,
nudge_x = 10 - na.omit(combined_list[[i]][combined_list[[i]]$PlotX > 0 & combined_list[[i]]$Dispensability < 0.1,]$PlotX),
segment.size = 0.2,
direction = "y",
hjust = 0) +
geom_text_repel(
data = na.omit(combined_list[[i]][combined_list[[i]]$PlotX < 0 & combined_list[[i]]$Dispensability < 0.1,]),
aes(PlotX, PlotY, label = Name, colour = name, size = Value), size =3.5,
nudge_x = -10 - na.omit(combined_list[[i]][combined_list[[i]]$PlotX < 0 & combined_list[[i]]$Dispensability < 0.1,]$PlotX),
segment.size = 0.2,
direction = "y",
hjust = 1) +
scale_color_manual(values = semspace.colors3[c(2,1,3)],
labels = c("DE & DS","DE only", "DS only"))+
labs (x = "Semantic space x", y = "Semantic space y") + theme(legend.key = element_blank()) +
xlim(-20,20) +
ylim(-9,9) +
theme(legend.position = "bottom") # This widens the right margin
print(p1)
})
plots3[[i]] <- local({
p1 <- ggplot( ) +
geom_point(data = combined_list[[i]][combined_list[[i]]$Value < log10(0.01), ], aes( PlotX, PlotY, size = PlotSize, colour = name ), alpha =0.75) +
geom_point( data = combined_list[[i]][combined_list[[i]]$Value < log10(0.01), ], aes(PlotX, PlotY, size = PlotSize), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) +
scale_color_manual(values = semspace.colors2[c(2,1,3)],
labels = c("DE & DS","DE only", "DS only"))+
scale_size( range=c(5, 20), guide = FALSE) +
theme_minimal(base_size = 15) +
new_scale_color() +
#geom_text_repel( data = combined_list[[i]][combined_list[[i]]$Dispensability < 0.001, ],
#aes(PlotX, PlotY, label = Name, colour = name), size = 4 ) +
geom_text_repel(
data = na.omit(combined_list[[i]][combined_list[[i]]$PlotX > 0 & combined_list[[i]]$Dispensability < 0.1 & combined_list[[i]]$Value < log10(0.01),]),
aes(PlotX, PlotY, label = Name, colour = name), size = 3.5,
nudge_x = 10 - na.omit(combined_list[[i]][combined_list[[i]]$PlotX > 0 & combined_list[[i]]$Dispensability < 0.1& combined_list[[i]]$Value < log10(0.01),]$PlotX) ,
segment.size = 0.2,
direction = "y",
hjust = 0) +
geom_text_repel(
data = na.omit(combined_list[[i]][combined_list[[i]]$PlotX < 0 & combined_list[[i]]$Dispensability < 0.1 & combined_list[[i]]$Value < log10(0.01),]),
aes(PlotX, PlotY, label = Name, colour = name, size = Value), size =3.5,
nudge_x = -10 - na.omit(combined_list[[i]][combined_list[[i]]$PlotX < 0 & combined_list[[i]]$Dispensability < 0.1 & combined_list[[i]]$Value < log10(0.01),]$PlotX),
segment.size = 0.2,
direction = "y",
hjust = 1) +
scale_color_manual(values = semspace.colors3[c(2,1,3)],
labels = c("DE & DS","DE only", "DS only"))+
labs (x = "Semantic space x", y = "Semantic space y") + theme(legend.key = element_blank()) +
xlim(-15,15) +
ylim(-9,9) +
theme(legend.position = "bottom")
print(p1)
})
}
## 1
## Warning: Removed 19 rows containing missing values (geom_point).
## Warning: Removed 19 rows containing missing values (geom_point).
## Warning: ggrepel: 7 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## 2
## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## 3
## 4
all_overlap <- plot_grid(plots2[[1]]+ theme(legend.position = "none"),
plots2[[2]]+ theme(legend.position = "none"),
plots2[[3]]+ theme(legend.position = "none"),
plots2[[4]]+ theme(legend.position = "none"),
ncol = 2, nrow =2, labels = c("A", "B", "C", "D"),
rel_widths = c(1,1), rel_heights = c(1,1))
## Warning: Removed 19 rows containing missing values (geom_point).
## Warning: Removed 19 rows containing missing values (geom_point).
ggsave(all_overlap, filename = "all_overlap_parchild_REVIGO_semspace.pdf", height = 12, width = 20)
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps
all_overlap_0.01 <- plot_grid(plots3[[1]]+ theme(legend.position = "none"),
plots3[[2]]+ theme(legend.position = "none"),
plots3[[3]]+ theme(legend.position = "none"),
plots3[[4]]+ theme(legend.position = "none"),
ncol = 2, nrow =2, labels = c("A", "B", "C", "D"),
rel_widths = c(1,1), rel_heights = c(1,1))
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
ggsave(all_overlap_0.01, filename = "all_overlap_0.01_parchild_REVIGO_semspace.pdf", height = 12, width = 20)
#### figure 2 plots ####
plots4 <- vector('list', length(combined_list))
plots5 <- vector('list', length(combined_list))
for (i in 1:length(combined_list)){
message(i)
plots4[[i]] <- local({
p1 <- ggplot( ) +
geom_point(data = combined_list[[i]], aes( PlotX, PlotY, size = PlotSize, colour = name ), alpha =0.75) +
geom_point( data = combined_list[[i]], aes(PlotX, PlotY, size = PlotSize), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) +
scale_color_manual(values = semspace.colors2[c(2,1,3)],
labels = c("DE & DS","DE only", "DS only"))+
scale_size( range=c(2, 10), guide = FALSE) +
labs(x = "Semantic Space X", y = "Semantic Space Y") +
theme_bw(base_size = 15)
print(p1)
})
plots5[[i]] <- local({
p1 <- ggplot( ) +
geom_point(data = combined_list[[i]][combined_list[[i]]$Value < log10(0.01), ], aes( PlotX, PlotY, size = PlotSize, colour = name ), alpha =0.75) +
geom_point( data = combined_list[[i]][combined_list[[i]]$Value < log10(0.01), ], aes(PlotX, PlotY, size = PlotSize), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) +
scale_color_manual(values = semspace.colors2[c(2,1,3)],
labels = c("DE & DS","DE only", "DS only"))+
scale_size( range=c(2, 10), guide = FALSE) +
labs(x = "Semantic Space X", y = "Semantic Space Y") +
theme_bw(base_size = 15)
print(p1)
})
}
## 1
## Warning: Removed 19 rows containing missing values (geom_point).
## Warning: Removed 19 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 1 rows containing missing values (geom_point).
## 2
## 3
## 4
save(plots4, file = paste0("Fig2_parchild_REVIGO_semspacePlots_family.Rdata"))
save(plots5, file = paste0("Fig2_0.01_parchild_REVIGO_semspacePlots_family.Rdata"))